Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Updated XLSX to CSV download #133

Merged
merged 1 commit into from
May 31, 2023
Merged

Updated XLSX to CSV download #133

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 2 additions & 1 deletion .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,8 @@
/.vscode/
/analysis/
/raw/
sample_metadata.xlsx
sample_metadata.csv


# Byte-compiled / optimized / DLL files
__pycache__/
Expand Down
131 changes: 63 additions & 68 deletions scripts/download_examples.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 4,
"id": "83673a33",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -63,14 +63,14 @@
" request.urlretrieve(\"https://zenodo.org/record/6449127/files/IMCWorkflow.ilp\", ilastik_project)\n",
" \n",
"# Sample metadata\n",
"sample_metadata = Path(\"..\") / \"sample_metadata.xlsx\"\n",
"sample_metadata = Path(\"..\") / \"sample_metadata.csv\"\n",
"if not sample_metadata.exists():\n",
" request.urlretrieve(\"https://zenodo.org/record/7575859/files/sample_metadata.csv\", sample_metadata)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 5,
"id": "5cebbf89",
"metadata": {},
"outputs": [
Expand All @@ -81,145 +81,140 @@
"# packages in environment at /Users/nils/opt/anaconda3/envs/imcsegpipe:\n",
"#\n",
"# Name Version Build Channel\n",
"aiofiles 22.1.0 pyhd8ed1ab_0 conda-forge\n",
"aiosqlite 0.18.0 pyhd8ed1ab_0 conda-forge\n",
"anyio 3.6.2 pyhd8ed1ab_0 conda-forge\n",
"appnope 0.1.3 pyhd8ed1ab_0 conda-forge\n",
"argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge\n",
"argon2-cffi-bindings 21.2.0 py39ha30fb19_3 conda-forge\n",
"asttokens 2.2.1 pyhd8ed1ab_0 conda-forge\n",
"attrs 22.2.0 pyh71513ae_0 conda-forge\n",
"async-lru 2.0.2 pyhd8ed1ab_0 conda-forge\n",
"attrs 23.1.0 pyh71513ae_1 conda-forge\n",
"babel 2.12.1 pyhd8ed1ab_1 conda-forge\n",
"backcall 0.2.0 pyh9f0ad1d_0 conda-forge\n",
"backports 1.0 pyhd8ed1ab_3 conda-forge\n",
"backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge\n",
"beautifulsoup4 4.11.2 pyha770c72_0 conda-forge\n",
"beautifulsoup4 4.12.2 pyha770c72_0 conda-forge\n",
"bleach 6.0.0 pyhd8ed1ab_0 conda-forge\n",
"brotlipy 0.7.0 py39ha30fb19_1005 conda-forge\n",
"brotli 1.0.9 hb7f2c08_8 conda-forge\n",
"brotli-bin 1.0.9 hb7f2c08_8 conda-forge\n",
"bzip2 1.0.8 h0d85af4_4 conda-forge\n",
"ca-certificates 2022.12.7 h033912b_0 conda-forge\n",
"certifi 2022.12.7 pyhd8ed1ab_0 conda-forge\n",
"ca-certificates 2023.5.7 h8857fd0_0 conda-forge\n",
"certifi 2023.5.7 pyhd8ed1ab_0 conda-forge\n",
"cffi 1.15.1 py39h131948b_3 conda-forge\n",
"charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge\n",
"comm 0.1.2 pyhd8ed1ab_0 conda-forge\n",
"cryptography 39.0.2 py39hbeae22c_0 conda-forge\n",
"debugpy 1.6.6 py39h7a8716b_0 conda-forge\n",
"charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge\n",
"comm 0.1.3 pyhd8ed1ab_0 conda-forge\n",
"debugpy 1.6.7 py39h7a8716b_0 conda-forge\n",
"decorator 5.1.1 pyhd8ed1ab_0 conda-forge\n",
"defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge\n",
"entrypoints 0.4 pyhd8ed1ab_0 conda-forge\n",
"executing 1.2.0 pyhd8ed1ab_0 conda-forge\n",
"flit-core 3.8.0 pyhd8ed1ab_0 conda-forge\n",
"flit-core 3.9.0 pyhd8ed1ab_0 conda-forge\n",
"idna 3.4 pyhd8ed1ab_0 conda-forge\n",
"imageio 2.26.0 pypi_0 pypi\n",
"imageio 2.30.0 pypi_0 pypi\n",
"imcsegpipe 1.0.0 pypi_0 pypi\n",
"importlib-metadata 6.0.0 pyha770c72_0 conda-forge\n",
"importlib_metadata 6.0.0 hd8ed1ab_0 conda-forge\n",
"importlib-metadata 6.6.0 pyha770c72_0 conda-forge\n",
"importlib_metadata 6.6.0 hd8ed1ab_0 conda-forge\n",
"importlib_resources 5.12.0 pyhd8ed1ab_0 conda-forge\n",
"ipykernel 6.21.2 pyh736e0ef_0 conda-forge\n",
"ipython 8.11.0 pyhd1c38e8_0 conda-forge\n",
"ipython_genutils 0.2.0 py_1 conda-forge\n",
"ipykernel 6.23.1 pyh736e0ef_0 conda-forge\n",
"ipython 8.13.2 pyhd1c38e8_0 conda-forge\n",
"jedi 0.18.2 pyhd8ed1ab_0 conda-forge\n",
"jinja2 3.1.2 pyhd8ed1ab_1 conda-forge\n",
"json5 0.9.5 pyh9f0ad1d_0 conda-forge\n",
"jsonschema 4.17.3 pyhd8ed1ab_0 conda-forge\n",
"jupyter_client 8.0.3 pyhd8ed1ab_0 conda-forge\n",
"jupyter_core 5.2.0 py39h6e9494a_0 conda-forge\n",
"jupyter-lsp 2.1.0 pyhd8ed1ab_0 conda-forge\n",
"jupyter_client 8.2.0 pyhd8ed1ab_0 conda-forge\n",
"jupyter_core 5.3.0 py39h6e9494a_0 conda-forge\n",
"jupyter_events 0.6.3 pyhd8ed1ab_0 conda-forge\n",
"jupyter_server 2.4.0 pyhd8ed1ab_0 conda-forge\n",
"jupyter_server_fileid 0.8.0 pyhd8ed1ab_0 conda-forge\n",
"jupyter_server 2.6.0 pyhd8ed1ab_0 conda-forge\n",
"jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge\n",
"jupyter_server_ydoc 0.6.1 pyhd8ed1ab_0 conda-forge\n",
"jupyter_ydoc 0.2.2 pyhd8ed1ab_0 conda-forge\n",
"jupyterlab 3.6.1 pyhd8ed1ab_0 conda-forge\n",
"jupyterlab 4.0.0 pyhd8ed1ab_1 conda-forge\n",
"jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge\n",
"jupyterlab_server 2.20.0 pyhd8ed1ab_0 conda-forge\n",
"jupyterlab_server 2.22.1 pyhd8ed1ab_0 conda-forge\n",
"jupytext 1.14.5 pyhcff175f_0 conda-forge\n",
"libcxx 15.0.7 h71dddab_0 conda-forge\n",
"libbrotlicommon 1.0.9 hb7f2c08_8 conda-forge\n",
"libbrotlidec 1.0.9 hb7f2c08_8 conda-forge\n",
"libbrotlienc 1.0.9 hb7f2c08_8 conda-forge\n",
"libcxx 16.0.4 hd57cbcb_0 conda-forge\n",
"libffi 3.4.2 h0d85af4_5 conda-forge\n",
"libsodium 1.0.18 hbcb3906_1 conda-forge\n",
"libsqlite 3.40.0 ha978bb4_0 conda-forge\n",
"libsqlite 3.42.0 h58db7d2_0 conda-forge\n",
"libzlib 1.2.13 hfd90126_4 conda-forge\n",
"markdown-it-py 2.2.0 pyhd8ed1ab_0 conda-forge\n",
"markupsafe 2.1.2 py39ha30fb19_0 conda-forge\n",
"matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge\n",
"mdit-py-plugins 0.3.5 pyhd8ed1ab_0 conda-forge\n",
"mdurl 0.1.0 pyhd8ed1ab_0 conda-forge\n",
"mistune 2.0.5 pyhd8ed1ab_0 conda-forge\n",
"nbclassic 0.5.3 pyhb4ecaf3_3 conda-forge\n",
"nbclient 0.7.2 pyhd8ed1ab_0 conda-forge\n",
"nbconvert 7.2.9 pyhd8ed1ab_0 conda-forge\n",
"nbconvert-core 7.2.9 pyhd8ed1ab_0 conda-forge\n",
"nbconvert-pandoc 7.2.9 pyhd8ed1ab_0 conda-forge\n",
"nbformat 5.7.3 pyhd8ed1ab_0 conda-forge\n",
"nbclient 0.8.0 pyhd8ed1ab_0 conda-forge\n",
"nbconvert-core 7.4.0 pyhd8ed1ab_0 conda-forge\n",
"nbformat 5.8.0 pyhd8ed1ab_0 conda-forge\n",
"ncurses 6.3 h96cf925_1 conda-forge\n",
"nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge\n",
"notebook 6.5.3 pyha770c72_0 conda-forge\n",
"notebook-shim 0.2.2 pyhd8ed1ab_0 conda-forge\n",
"numpy 1.24.2 pypi_0 pypi\n",
"openssl 3.0.8 hfd90126_0 conda-forge\n",
"packaging 23.0 pyhd8ed1ab_0 conda-forge\n",
"pandas 1.5.3 pypi_0 pypi\n",
"pandoc 2.19.2 h694c41f_2 conda-forge\n",
"notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge\n",
"numpy 1.24.3 pypi_0 pypi\n",
"openssl 3.1.0 h8a1eda9_3 conda-forge\n",
"overrides 7.3.1 pyhd8ed1ab_0 conda-forge\n",
"packaging 23.1 pyhd8ed1ab_0 conda-forge\n",
"pandas 2.0.2 pypi_0 pypi\n",
"pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge\n",
"parso 0.8.3 pyhd8ed1ab_0 conda-forge\n",
"pexpect 4.8.0 pyh1a96a4e_2 conda-forge\n",
"pickleshare 0.7.5 py_1003 conda-forge\n",
"pillow 9.4.0 pypi_0 pypi\n",
"pip 23.0.1 pyhd8ed1ab_0 conda-forge\n",
"pillow 9.5.0 pypi_0 pypi\n",
"pip 23.1.2 pyhd8ed1ab_0 conda-forge\n",
"pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge\n",
"platformdirs 3.1.0 pyhd8ed1ab_0 conda-forge\n",
"prometheus_client 0.16.0 pyhd8ed1ab_0 conda-forge\n",
"platformdirs 3.5.1 pyhd8ed1ab_0 conda-forge\n",
"prometheus_client 0.17.0 pyhd8ed1ab_0 conda-forge\n",
"prompt-toolkit 3.0.38 pyha770c72_0 conda-forge\n",
"prompt_toolkit 3.0.38 hd8ed1ab_0 conda-forge\n",
"psutil 5.9.4 py39ha30fb19_0 conda-forge\n",
"psutil 5.9.5 py39ha30fb19_0 conda-forge\n",
"ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge\n",
"pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge\n",
"pycparser 2.21 pyhd8ed1ab_0 conda-forge\n",
"pygments 2.14.0 pyhd8ed1ab_0 conda-forge\n",
"pyopenssl 23.0.0 pyhd8ed1ab_0 conda-forge\n",
"pygments 2.15.1 pyhd8ed1ab_0 conda-forge\n",
"pyobjc-core 9.1.1 py39h0504f80_0 conda-forge\n",
"pyobjc-framework-cocoa 9.1.1 py39h0504f80_0 conda-forge\n",
"pyrsistent 0.19.3 py39ha30fb19_0 conda-forge\n",
"pysocks 1.7.1 pyha2e5f31_6 conda-forge\n",
"python 3.9.16 h709bd14_0_cpython conda-forge\n",
"python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge\n",
"python-fastjsonschema 2.16.3 pyhd8ed1ab_0 conda-forge\n",
"python-fastjsonschema 2.17.1 pyhd8ed1ab_0 conda-forge\n",
"python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge\n",
"python_abi 3.9 3_cp39 conda-forge\n",
"pytz 2022.7.1 pyhd8ed1ab_0 conda-forge\n",
"pytz 2023.3 pyhd8ed1ab_0 conda-forge\n",
"pyyaml 6.0 py39ha30fb19_5 conda-forge\n",
"pyzmq 25.0.0 py39hed8f129_0 conda-forge\n",
"pyzmq 25.0.2 py39hed8f129_0 conda-forge\n",
"readimc 0.6.2 pypi_0 pypi\n",
"readline 8.1.2 h3899abd_0 conda-forge\n",
"requests 2.28.2 pyhd8ed1ab_0 conda-forge\n",
"readline 8.2 h9e318b2_1 conda-forge\n",
"requests 2.31.0 pyhd8ed1ab_0 conda-forge\n",
"rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge\n",
"rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge\n",
"scipy 1.10.1 pypi_0 pypi\n",
"send2trash 1.8.0 pyhd8ed1ab_0 conda-forge\n",
"setuptools 67.5.1 pyhd8ed1ab_0 conda-forge\n",
"send2trash 1.8.2 pyhd1c38e8_0 conda-forge\n",
"setuptools 67.7.2 pyhd8ed1ab_0 conda-forge\n",
"six 1.16.0 pyh6c4a22f_0 conda-forge\n",
"sniffio 1.3.0 pyhd8ed1ab_0 conda-forge\n",
"soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge\n",
"stack_data 0.6.2 pyhd8ed1ab_0 conda-forge\n",
"terminado 0.17.1 pyhd1c38e8_0 conda-forge\n",
"tifffile 2023.2.28 pypi_0 pypi\n",
"tifffile 2023.4.12 pypi_0 pypi\n",
"tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge\n",
"tk 8.6.12 h5dbffcc_0 conda-forge\n",
"toml 0.10.2 pyhd8ed1ab_0 conda-forge\n",
"tomli 2.0.1 pyhd8ed1ab_0 conda-forge\n",
"tornado 6.2 py39ha30fb19_1 conda-forge\n",
"tornado 6.3.2 py39hdc70f33_0 conda-forge\n",
"traitlets 5.9.0 pyhd8ed1ab_0 conda-forge\n",
"typing-extensions 4.4.0 hd8ed1ab_0 conda-forge\n",
"typing_extensions 4.4.0 pyha770c72_0 conda-forge\n",
"tzdata 2022g h191b570_0 conda-forge\n",
"urllib3 1.26.14 pyhd8ed1ab_0 conda-forge\n",
"typing-extensions 4.6.2 hd8ed1ab_0 conda-forge\n",
"typing_extensions 4.6.2 pyha770c72_0 conda-forge\n",
"typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge\n",
"tzdata 2023.3 pypi_0 pypi\n",
"urllib3 2.0.2 pyhd8ed1ab_0 conda-forge\n",
"wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge\n",
"webencodings 0.5.1 py_1 conda-forge\n",
"websocket-client 1.5.1 pyhd8ed1ab_0 conda-forge\n",
"wheel 0.38.4 pyhd8ed1ab_0 conda-forge\n",
"websocket-client 1.5.2 pyhd8ed1ab_0 conda-forge\n",
"wheel 0.40.0 pyhd8ed1ab_0 conda-forge\n",
"xtiff 0.7.9 pypi_0 pypi\n",
"xz 5.2.6 h775f41a_0 conda-forge\n",
"y-py 0.5.9 py39hd4bc93a_0 conda-forge\n",
"yaml 0.2.5 h0d85af4_2 conda-forge\n",
"ypy-websocket 0.8.2 pyhd8ed1ab_0 conda-forge\n",
"zeromq 4.3.4 he49afe7_1 conda-forge\n",
"zipp 3.15.0 pyhd8ed1ab_0 conda-forge\n"
]
Expand Down
2 changes: 1 addition & 1 deletion scripts/download_examples.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@
request.urlretrieve("https://zenodo.org/record/6449127/files/IMCWorkflow.ilp", ilastik_project)

# Sample metadata
sample_metadata = Path("..") / "sample_metadata.xlsx"
sample_metadata = Path("..") / "sample_metadata.csv"
if not sample_metadata.exists():
request.urlretrieve("https://zenodo.org/record/7575859/files/sample_metadata.csv", sample_metadata)

Expand Down
Loading